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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ), 'gf_id' => 'HOM05D001320', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001320' ), 'data_identifier' => 'HOM05D001320', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001320', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '475', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p02200' => 'bna', 'A03p25060' => 'bna', 'A04p01530' => 'bna', 'A07p02150' => 'bna', 'A07p23810' => 'bna', 'A09p00710' => 'bna', 'Aa31LG10G14920' => 'aar', 'Aa31LG1G26710' => 'aar', 'Aa31LG5G180' => 'aar', 'Aa31LG6G13520' => 'aar', 'Aa31LG8G15500' => 'aar', 'Actinidia02120' => 'ach', 'Actinidia12111' => 'ach', 'Actinidia12187' => 'ach', 'Actinidia14439' => 'ach', 'Actinidia18728' => 'ach', 'Actinidia22759' => 'ach', 'Actinidia22815' => 'ach', 'Actinidia27739' => 'ach', 'Ah.03g139300' => 'amhyb', 'Ah.07g203330' => 'amhyb', 'Ah.12g056730' => 'amhyb', 'AL4G44270' => 'aly', 'AL5G42940' => 'aly', 'AL6G53350' => 'aly', 'AL7G14300' => 'aly', 'Aqoxy5G03909' => 'aox', 'Aqoxy5G03910' => 'aox', 'Aqoxy6G01038' => 'aox', 'arahy.Tifrunner.gnm1.ann1.56KTIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIU33D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KSUC5C' => 'arhy', 'AT2G45160' => 'ath', 'AT3G60630' => 'ath', 'AT4G00150' => 'ath', 'AT4G36710' => 'ath', 'ATR0733G023' => 'atr', 'ATR0807G221' => 'atr', 'Atru.chr3.536' => 'acertr', 'Atru.chr5.254' => 'acertr', 'Atru.chr5.256' => 'acertr', 'Atru.chr9.1333' => 'acertr', 'Atru.chr9.1337' => 'acertr', 'AUR62007503' => 'cqu', 'AUR62008003' => 'cqu', 'AUR62039956' => 'cqu', 'BcaB01g02216' => 'bca', 'BcaB01g03287' => 'bca', 'BcaB02g07559' => 'bca', 'BcaB02g07561' => 'bca', 'BcaB03g16630' => 'bca', 'BcaC01g05154' => 'bca', 'BcaC02g10165' => 'bca', 'BcaC02g10166' => 'bca', 'BcaC04g24199' => 'bca', 'BcaC06g36424' => 'bca', 'BcaC08g44887' => 'bca', 'BcaNung00707' => 'bca', 'BcaNung04433' => 'bca', 'BcaNung06146' => 'bca', 'BcaNung06147' => 'bca', 'BolC1t00229H' => 'bol', 'BolC3t15337H' => 'bol', 'BolC4t24756H' => 'bol', 'BolC6t37658H' => 'bol', 'BolC7t40823H' => 'bol', 'BolC7t46610H' => 'bol', 'BolC9t52949H' => 'bol', 'BraA01t00208Z' => 'bra', 'BraA03t11708Z' => 'bra', 'BraA04t15873Z' => 'bra', 'BraA07t28010Z' => 'bra', 'BraA07t30032Z' => 'bra', 'BraA09t35689Z' => 'bra', 'C01p02390' => 'bna', 'C03p29900' => 'bna', 'C04p32030' => 'bna', 'C06p25020' => 'bna', 'C07p04280' => 'bna', 'C07p61880' => 'bna', 'C09p00140' => 'bna', 'CAN.G1218.13' => 'can', 'CAN.G1469.15' => 'can', 'CAN.G358.124' => 'can', 'CANSAT01G1227' => 'cansat', 'CANSAT21G1072' => 'cansat', 'CANSAT56G3983' => 'cansat', 'CANSAT56G4031' => 'cansat', 'CANSAT56G4337' => 'cansat', 'CARHR109150' => 'chi', 'CARHR140380' => 'chi', 'CARHR171030' => 'chi', 'CARHR245060' => 'chi', 'CARHR248190' => 'chi', 'Carub.0003s3274' => 'cru', 'Carub.0004s2777' => 'cru', 'Carub.0005s2736' => 'cru', 'Carub.0007s0361' => 'cru', 'Ca_02613_v3' => 'car', 'Ca_19834_v3' => 'car', 'Ca_26411_v3' => 'car', 'Cc02_g24390' => 'ccan', 'Cc07_g09180' => 'ccan', 'Cc08_g12670' => 'ccan', 'CDE04G1972' => 'cde', 'CDE09G0917' => 'cde', 'CDE11G0742' => 'cde', 'CDE12G0263' => 'cde', 'Cfa004280' => 'cfa', 'Cfa011171' => 'cfa', 'Cfa012742' => 'cfa', 'Ciclev10018916m.g' => 'ccl', 'Ciclev10019083m.g' => 'ccl', 'Ciclev10019094m.g' => 'ccl', 'Ciclev10025197m.g' => 'ccl', 'Ciclev10025246m.g' => 'ccl', 'CiPaw.01G034700' => 'cil', 'CiPaw.11G152700' => 'cil', 'CiPaw.13G032700' => 'cil', 'CiPaw.14G025900' => 'cil', 'ClCG06G003050' => 'cla', 'ClCG07G008970' => 'cla', 'ClCG07G008990' => 'cla', 'ClCG10G002760' => 'cla', 'COL.COLO4_12492' => 'col', 'COL.COLO4_22116' => 'col', 'Cpa.g.c34151' => 'cpa', 'Cpa.g.sc158.5' => 'cpa', 'Cpa.g.sc29.139' => 'cpa', 'Cpa.g.sc49.157' => 'cpa', 'CsaV3_3G002800' => 'csa', 'CsaV3_4G005220' => 'csa', 'CsaV3_4G005230' => 'csa', 'CsaV3_6G009170' => 'csa', 'CSS0000701' => 'camsi', 'CSS0004937' => 'camsi', 'CSS0010789' => 'camsi', 'CSS0017534' => 'camsi', 'CSS0019066' => 'camsi', 'CSS0037771' => 'camsi', 'CSS0048675' => 'camsi', 'DCAR_006824' => 'dca', 'DCAR_006825' => 'dca', 'DCAR_008485' => 'dca', 'DCAR_017151' => 'dca', 'DCAR_017238' => 'dca', 'Dinv03618' => 'din', 'Dinv06923' => 'din', 'Dinv13311' => 'din', 'Dinv17426' => 'din', 'Dinv21621' => 'din', 'Dinv26809' => 'din', 'Dinv39128' => 'din', 'Dinv39959' => 'din', 'Dinv43675' => 'din', 'Dinv44121' => 'din', 'Duzib068G0558' => 'dzi', 'Duzib084G0725' => 'dzi', 'Duzib133G0024' => 'dzi', 'Duzib138G0867' => 'dzi', 'Duzib147G0347' => 'dzi', 'Duzib187G0176' => 'dzi', 'Duzib205G1927' => 'dzi', 'Duzib264G0732' => 'dzi', 'ECA232G1591' => 'eca', 'ECA233G0712' => 'eca', 'ECA236G0390' => 'eca', 'ECA238G2667' => 'eca', 'ECA240G1936' => 'eca', 'EL10Ac5g13052' => 'bvu', 'EL10Ac6g14911' => 'bvu', 'Eucgr.E01509' => 'egr', 'Eucgr.E01510' => 'egr', 'Eucgr.H01257' => 'egr', 'FAN01G1998' => 'fan', 'FAN03G3091' => 'fan', 'FAN04G0481' => 'fan', 'FAN06G2625' => 'fan', 'FAN06G2903' => 'fan', 'FAN08G3518' => 'fan', 'FAN10G1866' => 'fan', 'FAN10G2195' => 'fan', 'FAN13G0128' => 'fan', 'FAN18G2925' => 'fan', 'FAN19G2573' => 'fan', 'FAN23G0620' => 'fan', 'FAN26G0597' => 'fan', 'FAN28G2314' => 'fan', 'FvH4_1g13740' => 'fve', 'FvH4_5g00020' => 'fve', 'FvH4_7g11120' => 'fve', 'Glyma.01G079500' => 'gma', 'Glyma.01G136300' => 'gma', 'Glyma.01G177200' => 'gma', 'Glyma.02G058700' => 'gma', 'Glyma.03G031800' => 'gma', 'Glyma.11G065200' => 'gma', 'Glyma.11G168219' => 'gma', 'Glyma.16G141300' => 'gma', 'Gohir.A02G163900' => 'ghi', 'Gohir.A03G008700' => 'ghi', 'Gohir.A08G172200' => 'ghi', 'Gohir.A10G094750' => 'ghi', 'Gohir.A12G094601' => 'ghi', 'Gohir.A12G094700' => 'ghi', 'Gohir.A12G220100' => 'ghi', 'Gohir.D03G016300' => 'ghi', 'Gohir.D03G162200' => 'ghi', 'Gohir.D08G190500' => 'ghi', 'Gohir.D10G093200' => 'ghi', 'Gohir.D12G097300' => 'ghi', 'Gohir.D12G097400' => 'ghi', 'Gohir.D12G222300' => 'ghi', 'Gorai.003G016500' => 'gra', 'Gorai.003G170700' => 'gra', 'Gorai.004G200600' => 'gra', 'Gorai.008G106000' => 'gra', 'Gorai.008G106100' => 'gra', 'Gorai.008G238300' => 'gra', 'Gorai.011G102400' => 'gra', 'GSVIVG01001308001' => 'vvi', 'GSVIVG01019006001' => 'vvi', 'GSVIVG01027680001' => 'vvi', 'HanXRQChr02g0049961' => 'han', 'HanXRQChr06g0169101' => 'han', 'HanXRQChr06g0170161' => 'han', 'HanXRQChr08g0228631' => 'han', 'HanXRQChr11g0324871' => 'han', 'HanXRQChr11g0326391' => 'han', 'HanXRQChr13g0396051' => 'han', 'HanXRQChr17g0563721' => 'han', 'Haze_02678' => 'cav', 'Haze_07886' => 'cav', 'Haze_15120' => 'cav', 'Haze_24911' => 'cav', 'Haze_24915' => 'cav', 'Hma1.2p1_0916F.1_g236500' => 'hma', 'Hma1.2p1_1635F.1_g294760' => 'hma', 'Hma1.2p1_2055F.1_g312770' => 'hma', 'Hma1.2p1_3707F.1_g337340' => 'hma', 'HPP92_002601' => 'vpl', 'HPP92_012815' => 'vpl', 'HPP92_014481' => 'vpl', 'HPP92_021283' => 'vpl', 'HPP92_022314' => 'vpl', 'HPP92_022324' => 'vpl', 'HPP92_023655' => 'vpl', 'Hund11590' => 'sun', 'Hund11591' => 'sun', 'Hund14579' => 'sun', 'Lalb_Chr07g0190221' => 'lal', 'Lalb_Chr07g0190241' => 'lal', 'Lalb_Chr09g0322591' => 'lal', 'Lalb_Chr12g0207921' => 'lal', 'Lalb_Chr12g0207931' => 'lal', 'Lalb_Chr13g0291841' => 'lal', 'Lj1g0000159' => 'lja', 'Lj2g0005342' => 'lja', 'Lj2P215T12' => 'lonja', 'Lj3g0003192' => 'lja', 'Lj3g0015276' => 'lja', 'Lj4g0026656' => 'lja', 'Lj4P197T11' => 'lonja', 'Lj7P535T15' => 'lonja', 'Lj7P535T17' => 'lonja', 'Lj9A610T64' => 'lonja', 'Lj9P565T37' => 'lonja', 'Lsat_1_v5_gn_2_76860' => 'lsa', 'Lsat_1_v5_gn_3_128721' => 'lsa', 'Lsat_1_v5_gn_3_681' => 'lsa', 'Lsat_1_v5_gn_3_78621' => 'lsa', 'Lsat_1_v5_gn_4_153400' => 'lsa', 'Lsat_1_v5_gn_6_3180' => 'lsa', 'Lsat_1_v5_gn_7_9261' => 'lsa', 'Manes.02G038400' => 'mes', 'Manes.05G048700' => 'mes', 'Manes.13G137100' => 'mes', 'MBI04_g41910_MAGBIO' => 'mbi', 'MBI04_g44457_MAGBIO' => 'mbi', 'MBI16_g37294_MAGBIO' => 'mbi', 'MD00G1043300' => 'mdo', 'MD02G1152200' => 'mdo', 'MD02G1210200' => 'mdo', 'MD04G1088100' => 'mdo', 'MD07G1115800' => 'mdo', 'MD15G1266500' => 'mdo', 'Medtr0092s0060' => 'mtr', 'Medtr0092s0100' => 'mtr', 'Medtr4g026485' => 'mtr', 'Medtr5g019750' => 'mtr', 'Medtr8g077940' => 'mtr', 'MELO3C013947.2' => 'cme', 'MELO3C017547.2' => 'cme', 'MELO3C017548.2' => 'cme', 'MELO3C021146.2' => 'cme', 'Migut.B01597' => 'egut', 'Migut.H00186' => 'egut', 'Migut.L00296' => 'egut', 'MSTRG.15279' => 'ama', 'MSTRG.17163' => 'ama', 'MSTRG.20730' => 'ama', 'MSTRG.23548' => 'ama', 'MSTRG.3582' => 'ama', 'Nitab4.5_0000312g0120' => 'nta', 'Nitab4.5_0000312g0160' => 'nta', 'Nitab4.5_0000859g0260' => 'nta', 'Nitab4.5_0001279g0120' => 'nta', 'Nitab4.5_0002128g0050' => 'nta', 'Nitab4.5_0011278g0010' => 'nta', 'Nitab4.5_0012398g0010' => 'nta', 'Nitab4.5_0012398g0020' => 'nta', 'Nn1g01046' => 'nnu', 'Nn1g03518' => 'nnu', 'Nn4g24457' => 'nnu', 'Nn5g29532' => 'nnu', 'Oeu000018.2' => 'oeu', 'Oeu004549.1' => 'oeu', 'Oeu021564.2' => 'oeu', 'Oeu026411.2' => 'oeu', 'Oeu032183.1' => 'oeu', 'Oeu035396.1' => 'oeu', 'Oeu037895.1' => 'oeu', 'Oeu040217.1' => 'oeu', 'Oeu044570.1' => 'oeu', 'Oeu053003.2' => 'oeu', 'Oeu064173.2' => 'oeu', 'Os02g0662700' => 'osa', 'Os02g0663100' => 'osa', 'Os03g0103400' => 'osa', 'Os04g0555000' => 'osa', 'Os06g0105350' => 'osa', 'Os10g0551200' => 'osa', 'Peaxi162Scf00002g00162' => 'pax', 'Peaxi162Scf00427g00052' => 'pax', 'Peaxi162Scf00803g00003' => 'pax', 'PGR042G0628' => 'pgr', 'PGR102G1006' => 'pgr', 'PGSC0003DMG400004752' => 'stu', 'PGSC0003DMG400012683' => 'stu', 'PGSC0003DMG400025973' => 'stu', 'Phvul.002G027500' => 'pvu', 'Phvul.003G252200' => 'pvu', 'Phvul.008G143400' => 'pvu', 'Phvul.010G072700' => 'pvu', 'Phvul.010G072900' => 'pvu', 'Potri.001G122800' => 'ptr', 'Potri.002G144200' => 'ptr', 'Potri.002G144700' => 'ptr', 'Potri.003G110800' => 'ptr', 'Potri.005G125800' => 'ptr', 'Potri.007G029200' => 'ptr', 'Potri.014G060200' => 'ptr', 'Potri.014G060500' => 'ptr', 'Prupe.2G138400' => 'ppe', 'Prupe.5G072300' => 'ppe', 'Prupe.7G150900' => 'ppe', 'Psat3g163480' => 'psa', 'Psat4g091760' => 'psa', 'PSO017G7339' => 'pso', 'PSO170G0403' => 'pso', 'PSO339G2716' => 'pso', 'PSO384G3952' => 'pso', 'QL04p038785' => 'qlo', 'QL04p038815' => 'qlo', 'QL04p038841' => 'qlo', 'QL06p045373' => 'qlo', 'QL12p012621' => 'qlo', 'RcHm_v2.0_Chr1g0349141' => 'rch', 'RcHm_v2.0_Chr2g0102171' => 'rch', 'RcHm_v2.0_Chr7g0202931' => 'rch', 'Rhsim01G0150800' => 'rsi', 'Rhsim07G0030900' => 'rsi', 'Sabra01G0094600' => 'sbr', 'Sabra02G0112600' => 'sbr', 'Sabra03G0076900' => 'sbr', 'Sabra05G0103500' => 'sbr', 'Sabra07G0025100' => 'sbr', 'Sabra14G0044100' => 'sbr', 'Sabra14G0044400' => 'sbr', 'SalBow5G2653' => 'sbo', 'SalBow5G3328' => 'sbo', 'SalBow5G5278' => 'sbo', 'Sc01g0008540' => 'sci', 'Sc03g0000890' => 'sci', 'Sc07g0009330' => 'sci', 'Sc16g0001120' => 'sci', 'Sc22g0000800' => 'sci', 'Sed0003392' => 'sed', 'Sed0013118' => 'sed', 'Sed0017132' => 'sed', 'SEGI_02575' => 'sgi', 'SEGI_23419' => 'sgi', 'SGA_v2.0_scaffold153G36971' => 'sas', 'SGA_v2.0_scaffold33G13392' => 'sas', 'SGA_v2.0_scaffold399G50791' => 'sas', 'SGA_v2.0_scaffold43G16508' => 'sas', 'SHI08673' => 'shi', 'SHI09608' => 'shi', 'Solyc01g090950.4' => 'sly', 'Solyc02g085600.1' => 'sly', 'Solyc08g078800.1' => 'sly', 'Sopen01g036680' => 'spe', 'Sopen02g030270' => 'spe', 'Sopen08g027270' => 'spe', 'Sp3g32000' => 'spa', 'Sp5g02610' => 'spa', 'Sp6g00220' => 'spa', 'Sp7g34370' => 'spa', 'SpUn0031_0110' => 'spa', 'TAR374G0827' => 'tar', 'TAR375G0065' => 'tar', 'TAR375G0243' => 'tar', 'TAR375G0290' => 'tar', 'TAR375G1060' => 'tar', 'TAR381G1338' => 'tar', 'TAR629G3148' => 'tar', 'TAR636G1008' => 'tar', 'THA.LOC104802467' => 'tha', 'THA.LOC104807544' => 'tha', 'THA.LOC104817010' => 'tha', 'THA.LOC104817221' => 'tha', 'THA.LOC104819799' => 'tha', 'Thecc.01G039700' => 'tca', 'Thecc.01G382400' => 'tca', 'Thecc.03G253700' => 'tca', 'Thhalv10001784m.g' => 'esa', 'Thhalv10006506m.g' => 'esa', 'Thhalv10023133m.g' => 'esa', 'Thhalv10025054m.g' => 'esa', 'Thhalv10029148m.g' => 'esa', 'TPR.G20270' => 'tpr', 'TPR.G39098' => 'tpr', 'TPR.G5027' => 'tpr', 'TWI09G0309' => 'twi', 'TWI14G0097' => 'twi', 'TWI23G0829' => 'twi', 'TWI59G0954' => 'twi', 'TWI73G0412' => 'twi', 'unitig_0.g1308' => 'ugi', 'unitig_22.g5387' => 'ugi', 'unitig_26.g8893' => 'ugi', 'unitig_26.g8894' => 'ugi', 'unitig_37.g12368' => 'ugi', 'unitig_748.g8519' => 'ugi', 'unitig_749.g14383' => 'ugi', 'unitig_76.g29080' => 'ugi', 'unitig_8.g3827' => 'ugi', 'unitig_8.g3828' => 'ugi', 'vmacro13439' => 'vma', 'vmacro21029' => 'vma', 'VMungo0331G0016' => 'vmu', 'VMungo0331G1322' => 'vmu', 'VMungo1215G3057' => 'vmu', 'VMungo1383G3366' => 'vmu', 'Zm00001eb000470' => 'zma', 'Zm00001eb002990' => 'zma', 'Zm00001eb023010' => 'zma', 'Zm00001eb067930' => 'zma', 'Zm00001eb067940' => 'zma', 'Zm00001eb067950' => 'zma', 'Zm00001eb071420' => 'zma', 'Zm00001eb074460' => 'zma', 'Zm00001eb186770' => 'zma', 'Zm00001eb249840' => 'zma', 'Zm00001eb268460' => 'zma', 'Zm00001eb268470' => 'zma', 'Zm00001eb301400' => 'zma', 'Zm00001eb301410' => 'zma', 'Zm00001eb326550' => 'zma', 'Zm00001eb327660' => 'zma', 'Zm00001eb366160' => 'zma', 'Zm00001eb379340' => 'zma', 'Zm00001eb398990' => 'zma', 'Zm00001eb399000' => 'zma', 'Zm00001eb429450' => 'zma' ) $gf_id = 'HOM05D001320' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001320' ) $data_identifier = 'HOM05D001320' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 3, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 3, 'bca' => (int) 15, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 5, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 3, 'mbi' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppe' => (int) 3, 'psa' => (int) 2, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 10, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 21 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb429450' $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